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Coding Skills

R
Python
Bash
AWK
SQL
Perl

R: tidyverse, data.table, Shiny, plotly, tidymodels, caret and others
Python: NumPy, Pandas, SciPy, scikit-learn, keras, PyTorch, Seaborn, matplotlib and more

Languages

Polish
English
French

Disclaimer

Made with the R package pagedown.

Based on the Nick Strayer’s CV package; modified source code for this CV is available here.

Last updated on 2022-11-25.

Main

Kasia Kedzierska

I am a PhD student at the University of Oxford. As a computational biologist, I use Data Science and Machine Learning to answer biological questions. Specifically, I study cancer of the uterus and chromatin organisation in disease progression. Last summer, I joined Computational Biology Department at Novo Nordisk Research Centre in Oxford as an intern, where I was working with NLP methods and knowledge graphs. Currently, I am looking into adapting my experience from the internship to build models for investigating cancer evolution.

Selected Research Experience

Intern

Novo Nordisk Research Centre Oxford

Oxford, United Kingdom

2021

  • I used NLP based methods to screen biomedical articles and identify potential therapeutic targets. I built R Shiny App to allow colleagues within the company to investigate results from our pipeline.

DPhil Candidate

Wellcome Centre for Human Genetics, Big Data Institute

University of Oxford, UK

present - 2018

  • In my PhD project Functional and evolutionary characterisation of chromatin organisation in endometrial cancer I am looking at how chromatin organisation influences disease progression in cancer of the uterus.
  • Mentored by D. Church and D. Woodcock
  • Currently I’m working on building and refining ML models of cancer evolution.

Visiting Graduate Student

Ratan group

University of Virginia, USA

2018 - 2017

  • Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays.
  • Worked on the Master thesis - Analysis of the mutational burden across gene sets in cancer.

Education

DPhil. Candidate, Genomic Medicine and Statistics

Nuffield Department of Medicine, Brasenose College

University of Oxford, UK

present - 2018

M. Sc. Eng., Biotechnology

Warsaw University of Technology

Warsaw, Poland

2018 - 2015

  • Master thesis: - Analysis of the mutational burden across gene sets in cancer awarded the title of The Best Master Thesis in Bioinformatics defended in 2018.

Selected Publications

Full list of publication on my Google Scholar profile scholar.google.com/citations?user=Yv6poTwAAAAJ.

Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift

M. Migdal, E. Tralle, K. A. Nahia, L. Bugajski, K. Z. Kedzierska, F. Garbicz, K. Piwocka, C. L. Winata, M. Pawlak

BMC Genomics

2021

The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability

H. Russell, K. Kedzierska, D. D. Buchanan, R. Thomas, E. Tham, M. Mints, A. Keränen, G. G. Giles, M. C. Southey, R. L. Milne, I. Tomlinson, D. Church, A. B. Spurdle, T. A. O’Mara and A. Lewis

Clinical Epigenetics

2020

Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

M. Pawlak, K. Z. Kedzierska, M. Migdal, K. A. Nahia, J. A. Ramilowski, L. Bugajski, K. Hashimoto, A. Marconi, K. Piwocka, P. Carninci and C. L. Winata

Genome Research

2019

SONiCS: PCR stutter noise correction in genome-scale microsatellites

K. Z. Kedzierska, L. Gerber, D. Cagnazzi, M. Krützen, A. Ratan, L. Kistler

Bioinformatics

2018

Selected Talks and Posters

Systematic characterisation of chromatin modifiers in endometrial cancer

European Association for Cancer Research 2022 Congress

Seville, Spain

2022

Analysis of the mutational burden across gene sets in cancer

Polish Bioinformatics Society Symposium

Cracow, Poland

2019

  • Invited talk

Differential mutation analysis across gene sets in cancers

Biology of Genomes 2018

Cold Spring Harbor, NY, USA

2018

  • Poster

Selected Awards and Honours

Senior Hulme Scholarship

Brasenose College, University of Oxford

Oxford, UK

present - 2021

  • Senior Hulme Scholarship is awarded by Brasenose College, University of Oxford to DPhil students whose academic performance is deemed to be exceptional.

Graduate Prize in the ‘Outstanding work outside degree’ category

Nuffield Department of Medicine, University of Oxford

Oxford, UK

2022 - 2021

  • Each year Nuffield Department of Medicine, based on nominations, awards selected PhD students based on their performance within and outside of their degree.

Attended Workshops, Summer Schools

Machine Learning Summer School

Imperial College London, University College London

London, United Kingdom

2019

Teaching Experience

Unsupervised learning

NGSchool2022: Machine Learning in Computational Biology

Jablonna, Poland

2022

Data visualization in bioinformatics - hackathon mentor

Online hackathon NGSprint

Discord

2021

  • I led the hackathon in data viusalisation with emphasis on computational biology. Under my supervision, 3 teams of around 5 people each, created interactive and captivating visualisation. Teaching materials are available at github.com/kzkedzierska/NGSprint_data_viz.

Online tutorials: Python for Data Science and Introduction to Python

NGSeminars

YouTube

2020

Introduction to R

Wellcome Centre for Human Genetics

Oxford, United Kingdom

2019

  • 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
  • Materials available on github/kzkedziersa/r_intro

Introduction to Managing Code with Git

Wellcome Centre for Human Genetics

Oxford, United Kingdom

2020 - 2019

Selected Grants

Visegrad Grant to organize NGSchool2022

Visegrad Fund

N/A

2022 - 2020

  • 32,190 EUR awarded towards organising affordable training and conference focusing on ML application in Computational Biology. During this project I managed an international team of volunteers and led the organisation of summer school, conference, online seminars and hackathon.

Non-profit Work

President

NGSchool Society

N/A

present - 2018

  • The goal of the Society is to promote and support science, with emphasis on computational biology.
  • President since 2019; Vice President 2018 - 2019, Founder